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Showing NP-Card for l-ribonic acid (NP0305526)

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Record Information
Version2.0
Created at2022-09-10 21:25:58 UTC
Updated at2022-09-10 21:25:59 UTC
NP-MRD IDNP0305526
Secondary Accession NumbersNone
Natural Product Identification
Common Namel-ribonic acid
DescriptionL-ribonic acid, also known as L-ribonate, belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. L-ribonic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. l-ribonic acid was first documented in 2018 (PMID: 29468297). Based on a literature review very few articles have been published on L-ribonic acid.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0305526 (l-ribonic acid)


  Mrv1652309102223252D          

 11 10  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
Download

3D MOL for NP0305526 (l-ribonic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
    2.3514   -0.8890   -1.5659 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0656   -0.3603   -0.4624 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6903   -0.8938    0.6550 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1131    0.7771   -0.3277 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5946    1.1711   -1.5309 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0518    0.5084    0.6976 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7189    1.6453    0.9072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7497   -0.7404    0.4867 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4974   -0.8955    1.6945 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7678   -0.6767   -0.5982 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2876   -0.5495   -1.8784 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6551   -0.7086    0.8940 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7255    1.6266    0.1021 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1511    0.7627   -2.2616 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6408    0.4043    1.6778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7745    2.2266    0.0989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1429   -1.6368    0.3973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2510   -0.2646    1.6527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5496    0.1171   -0.4019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3758   -1.6287   -0.5842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9240    0.0047   -2.4144 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10  8  1  0
  8  9  1  0
  8  6  1  0
  6  7  1  0
  6  4  1  0
  4  5  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
 11 21  1  0
 10 19  1  0
 10 20  1  0
  8 17  1  6
  9 18  1  0
  6 15  1  1
  7 16  1  0
  4 13  1  1
  5 14  1  0
  3 12  1  0
M  END
Download

3D SDF for NP0305526 (l-ribonic acid)


  Mrv1652309102223252D          

 11 10  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0305526

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H](O)[C@H](O)[C@H](O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3-,4-/m0/s1

> <INCHI_KEY>
QXKAIJAYHKCRRA-HZLVTQRSSA-N

> <FORMULA>
C5H10O6

> <MOLECULAR_WEIGHT>
166.129

> <EXACT_MASS>
166.047738042

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.306742463625213

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S)-2,3,4,5-tetrahydroxypentanoic acid

> <JCHEM_LOGP>
-2.7794093686666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.768659694136133

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3931398115505433

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974562302797298

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
32.3085

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4S)-2,3,4,5-tetrahydroxypentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0305526 (l-ribonic acid)

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PDB for NP0305526 (l-ribonic acid)
HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0305526 (l-ribonic acid)
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SMILES for NP0305526 (l-ribonic acid)
OC[C@H](O)[C@H](O)[C@H](O)C(O)=O
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INCHI for NP0305526 (l-ribonic acid)
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3-,4-/m0/s1
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View in JSmol
Synonyms
ValueSource
L-RibonateGenerator
Chemical FormulaC5H10O6
Average Mass166.1290 Da
Monoisotopic Mass166.04774 Da
IUPAC Name(2S,3S,4S)-2,3,4,5-tetrahydroxypentanoic acid
Traditional Name(2S,3S,4S)-2,3,4,5-tetrahydroxypentanoic acid
CAS Registry NumberNot Available
SMILES
OC[C@H](O)[C@H](O)[C@H](O)C(O)=O
InChI Identifier
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3-,4-/m0/s1
InChI KeyQXKAIJAYHKCRRA-HZLVTQRSSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentSugar acids and derivatives  
Alternative Parents
Substituents
  • Pentose monosaccharide
    • 

  • Beta-hydroxy acid
    • 

  • Sugar acid
    • 

  • Short-chain hydroxy acid
    • 

  • Alpha-hydroxy acid
    • 

  • Fatty acid
    • 

  • Hydroxy acid
    • 

  • Monosaccharide
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Polyol
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.8ChemAxon
pKa (Strongest Acidic)3.39ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area118.22 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.31 m³·mol⁻¹ChemAxon
Polarizability14.31 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00054455  
Chemspider ID5341919  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6971040  
PDB IDNot Available
ChEBI ID87765  
Good Scents IDNot Available
References
General References
  1. Yakushi T, Terada Y, Ozaki S, Kataoka N, Akakabe Y, Adachi O, Matsutani M, Matsushita K: Aldopentoses as new substrates for the membrane-bound, pyrroloquinoline quinone-dependent glycerol (polyol) dehydrogenase of Gluconobacter sp. Appl Microbiol Biotechnol. 2018 Apr;102(7):3159-3171. doi: 10.1007/s00253-018-8848-1. Epub 2018 Feb 21. [PubMed:29468297  ] 
  2. LOTUS database [Link]